Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

304 Chapter 6: How Cells Read the Genome: From DNA to Protein
base-pairing. In this way, the growing RNA chain is extended by one nucleotide
at a time in the 5ʹ-to-3ʹ direction (Figure 6–9). The substrates are ribonucleoside
triphosphates (ATP, CTP, UTP, and GTP); as in DNA replication, the hydrolysis of
high-energy bonds provides the energy needed to drive the reaction forward (see
Figure 5–4 and Movie 6.2).
The almost immediate release of the RNA strand from the DNA as it is synthesized
means that many RNA copies can be made from the same gene in a relatively
short time, with the synthesis of additional RNA molecules being started before
the previous RNA molecules are completed (Figure 6–10). When RNA polymerase
molecules follow hard on each other’s heels in this way, each moving at about
50 nucleotides per second, over a thousand transcripts can be synthesized in an
hour from a single gene.
Although RNA polymerase catalyzes essentially the same chemical reaction as
DNA polymerase, there are some important differences between the activities of
the two enzymes. First, and most obviously, RNA polymerase catalyzes the linkage
of ribonucleotides, not deoxyribonucleotides. Second, unlike the DNA polymerases
involved in DNA replication, RNA polymerases can start an RNA chain
without a primer. This difference is thought possible because transcription need
not be as accurate as DNA replication (see Table 5–1, p. 244). RNA polymerases
make about one mistake for every 10 4 nucleotides copied into RNA (compared
with an error rate for direct copying by DNA polymerase of about one in 10 7 nucleotides);
and the consequences of an error in RNA transcription are much less significant
as RNA does not permanently store genetic information in cells. Finally,
unlike DNA polymerases, which make their products in segments that are later
stitched together, RNA polymerases are absolutely processive; that is, the same
RNA polymerase that begins an RNA molecule must finish it without dissociating
from the DNA template.
Although not nearly as accurate as the DNA polymerases that replicate DNA,
RNA polymerases nonetheless have a modest proofreading mechanism. If an
incorrect ribonucleotide is added to the growing RNA chain, the polymerase can
back up, and the active site of the enzyme can perform an excision reaction that
resembles the reverse of the polymerization reaction, except that a water molecule
replaces the pyrophosphate and a nucleoside monophosphate is released.
Given that DNA and RNA polymerases both carry out template-dependent
nucleotide polymerization, it might be expected that the two types of enzymes
would be structurally related. However, x-ray crystallographic studies reveal that,
other than containing a critical Mg 2+ ion at the catalytic site, the two enzymes are
quite different. Template-dependent nucleotide-polymerizing enzymes seem to
have arisen at least twice during the early evolution of cells. One lineage led to the
newly synthesized
RNA transcript
5′
template
DNA strand
5′
3′
Mg 2+ at
active site
RNA polymerase
short region of
DNA/RNA helix
ribonucleoside
triphosphate uptake
channel
downstream
DNA double helix
3′
5′
direction of
transcription
DNA
5′ 3′
3′ 5′
template strand
RNA
TRANSCRIPTION
5′ 3′
Figure 6–8 DNA transcription produces
a single-stranded RNA molecule that
is complementary to one strand of the
DNA double helix. Note that the sequence
of bases in the RNA molecule produced is
the same as the sequence of bases in the
non-template DNA strand, except that a U
replaces every T MBoC6 base m6.07/6.07
in the DNA.
Figure 6–9 DNA is transcribed by the
enzyme RNA polymerase. The RNA
polymerase (pale blue) moves stepwise
along the DNA, unwinding the DNA helix
at its active site indicated by the Mg 2+
(red), which is required for catalysis.
As it progresses, the polymerase adds
nucleotides one by one to the RNA chain at
the polymerization site, using an exposed
DNA strand as a template. The RNA
transcript is thus a complementary copy of
one of the two DNA strands. A short region
of DNA/RNA helix (approximately nine
nucleotide pairs in length) is formed only
transiently, and a “window” of DNA/RNA
helix therefore moves along the DNA with
the polymerase as the DNA double helix
reforms behind it. The incoming nucleotides
are in the form of ribonucleoside
triphosphates (ATP, UTP, CTP, and GTP),
and the energy stored in their phosphate–
phosphate bonds provides the driving
force for the polymerization reaction (see
Figure 5–4). The figure, based on an x-ray
crystallographic structure, shows a cutaway
view of the polymerase: the part
facing the viewer has been sliced away
to reveal the interior (Movie 6.3).
(Adapted from P. Cramer et al., Science
288:640–649, 2000; PDB code: 1HQM.)